› 4q0b

X-ray diffraction
3.3Å resolution

Crystal structure of HIV-1 reverse transcriptase in complex with gap-RNA/DNA and Nevirapine

Released:
DOI: 10.2210/pdb4q0b/pdb
PDB entry 4q0b coloured by chain, front view.
PDB entry 4q0b coloured by chain, side view.
PDB entry 4q0b coloured by chain, top view.
Source organism: Human immunodeficiency virus type 1 BH10
Primary publication:
Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage.
Das K, Martinez SE, Bandwar RP, Arnold E
OpenAccess logo Nucleic Acids Res 42 8125-37 (2014)
PMID: 24880687

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-508871 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
2 distinct RNA molecules
Macromolecules (5 distinct):
Reverse transcriptase/ribonuclease H Chains: A, C
Molecule details ›
Chains: A, C
Length: 556 amino acids
Theoretical weight: 64.02 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1153; Coverage: 38%)
Gene name: gag-pol
Sequence domains:
Structure domains:
p51 RT Chains: B, D
Molecule details ›
Chains: B, D
Length: 428 amino acids
Theoretical weight: 50.04 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1027; Coverage: 30%)
Gene name: gag-pol
Sequence domains:
Structure domains:
5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*G)-3' Chains: F, P
Molecule details ›
Chains: F, P
Length: 21 nucleotides
Theoretical weight: 6.42 KDa
5'-R(*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*G)-3' Chains: E, T
Molecule details ›
Chains: E, T
Length: 14 nucleotides
Theoretical weight: 4.49 KDa
5'-R(P*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3' Chains: e, t
Molecule details ›
Chains: e, t
Length: 12 nucleotides
Theoretical weight: 3.89 KDa

Ligands and Environments

3 bound ligands:
Ligand NVP 2 x NVP
Ligand MN 2 x MN
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P21
Unit cell:
a: 89.716Å b: 131.051Å c: 141.631Å
α: 90° β: 100.69° γ: 90°
R-values:
R R work R free
0.237 0.235 0.317
Expression system: Escherichia coli

Quick links

Citations

5 review citations

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Šponer et al. (2018)
4 more

6 mentions without citation

Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review.
Tarasova et al. (2018)
5 more